-
1
-
-
0026345750
-
Folding of chymotrypsin inhibitor 2.1. Evidence for a two-state transition
-
Jackson SE, Fersht AR. Folding of chymotrypsin inhibitor 2.1. Evidence for a two-state transition. Biochemistry 1991;30:10428-10435.
-
(1991)
Biochemistry
, vol.30
, pp. 10428-10435
-
-
Jackson, S.E.1
Fersht, A.R.2
-
2
-
-
0034604105
-
A surprising simplicity to protein folding
-
Baker D. A surprising simplicity to protein folding. Nature 2000;405:39-42.
-
(2000)
Nature
, vol.405
, pp. 39-42
-
-
Baker, D.1
-
3
-
-
0034284366
-
Modeling protein density of states: Additive hydrophobic effects are insufficient for calorimetric two-state cooperativity
-
Chan HS. Modeling protein density of states: additive hydrophobic effects are insufficient for calorimetric two-state cooperativity. Proteins 2000;40:543-571.
-
(2000)
Proteins
, vol.40
, pp. 543-571
-
-
Chan, H.S.1
-
4
-
-
0034284060
-
Polymer principles of protein calorimetric two-state cooperativity
-
Erratum: Proteins 2001;43:523
-
Kaya H, Chan HS. Polymer principles of protein calorimetric two-state cooperativity. Proteins 2000;40:637-661 [Erratum: Proteins 2001;43:523].
-
(2000)
Proteins
, vol.40
, pp. 637-661
-
-
Kaya, H.1
Chan, H.S.2
-
5
-
-
0034310589
-
Energetic components of cooperative protein folding
-
Kaya H, Chan HS. Energetic components of cooperative protein folding. Phys Rev Lett 2000;85:4823-4826.
-
(2000)
Phys Rev Lett
, vol.85
, pp. 4823-4826
-
-
Kaya, H.1
Chan, H.S.2
-
6
-
-
0036304480
-
Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: How applicable is the transition state picture to folding and unfolding?
-
Kaya H, Chan HS. Towards a consistent modeling of protein thermodynamic and kinetic cooperativity: how applicable is the transition state picture to folding and unfolding? J Mol Biol 2002;315:899-909.
-
(2002)
J Mol Biol
, vol.315
, pp. 899-909
-
-
Kaya, H.1
Chan, H.S.2
-
7
-
-
0002134029
-
Computational methods for protein folding: Scaling a hierarchy of complexities
-
Jiang T, Xu Y, Zhang MQ, editors. Cambridge, MA: The MIT Press
-
Chan HS, Kaya H, Shimizu S. Computational methods for protein folding: scaling a hierarchy of complexities. In: Jiang T, Xu Y, Zhang MQ, editors. Current Topics in Computational Molecular Biology. Cambridge, MA: The MIT Press; 2002. p 403-447.
-
(2002)
Current Topics in Computational Molecular Biology
, pp. 403-447
-
-
Chan, H.S.1
Kaya, H.2
Shimizu, S.3
-
8
-
-
0037459035
-
Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: How adequate is native-centric topological modeling?
-
Kaya H, Chan HS. Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: how adequate is native-centric topological modeling? J Mol Biol 2003;326:911-931.
-
(2003)
J Mol Biol
, vol.326
, pp. 911-931
-
-
Kaya, H.1
Chan, H.S.2
-
9
-
-
0042093787
-
Origins of chevron rollovers in non-two-state protein folding kinetics
-
Kaya H, Chan HS. Origins of chevron rollovers in non-two-state protein folding kinetics. Phys Rev Lett 2003;90:258104.
-
(2003)
Phys Rev Lett
, vol.90
, pp. 258104
-
-
Kaya, H.1
Chan, H.S.2
-
10
-
-
0042130544
-
Simple two-state protein folding kinetics requires near-Levinthal thermodynamic cooperativity
-
Kaya H, Chan HS. Simple two-state protein folding kinetics requires near-Levinthal thermodynamic cooperativity. Proteins 2003;52:510-523.
-
(2003)
Proteins
, vol.52
, pp. 510-523
-
-
Kaya, H.1
Chan, H.S.2
-
11
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein folding: A synthesis
-
Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins 1995;21:167-195.
-
(1995)
Proteins
, vol.21
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
12
-
-
0028929556
-
Principles of protein folding - A perspective from simple exact models
-
Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS. Principles of protein folding - a perspective from simple exact models. Protein Sci 1995;4:561-602.
-
(1995)
Protein Sci
, vol.4
, pp. 561-602
-
-
Dill, K.A.1
Bromberg, S.2
Yue, K.3
Fiebig, K.M.4
Yee, D.P.5
Thomas, P.D.6
Chan, H.S.7
-
13
-
-
0001103473
-
Kinetics of folding of proteins and RNA
-
Thirumalai D, Woodson SA. Kinetics of folding of proteins and RNA. Acc Chem Res 1996;29:433-439.
-
(1996)
Acc Chem Res
, vol.29
, pp. 433-439
-
-
Thirumalai, D.1
Woodson, S.A.2
-
14
-
-
0003166498
-
Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics
-
Chan HS, Dill KA. Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics. Proteins 1998;30:2-33.
-
(1998)
Proteins
, vol.30
, pp. 2-33
-
-
Chan, H.S.1
Dill, K.A.2
-
15
-
-
0034984144
-
Protein folding theory: From lattice to all-atom models
-
Mirny L, Shakhnovich E. Protein folding theory: from lattice to all-atom models. Annu Rev Biophys Biomol Struct 2001;30:361-396.
-
(2001)
Annu Rev Biophys Biomol Struct
, vol.30
, pp. 361-396
-
-
Mirny, L.1
Shakhnovich, E.2
-
16
-
-
0032502839
-
Contact order, transition state placement and the refolding rates of single domain proteins
-
Plaxco KW, Simons KT, Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 1998;227:985-994.
-
(1998)
J Mol Biol
, vol.227
, pp. 985-994
-
-
Plaxco, K.W.1
Simons, K.T.2
Baker, D.3
-
17
-
-
0032559928
-
Matching speed and locality
-
Chan HS. Matching speed and locality. Nature 1998;392:761-763.
-
(1998)
Nature
, vol.392
, pp. 761-763
-
-
Chan, H.S.1
-
18
-
-
0034687123
-
Topology, stability, sequence, and length: Defining the determinants of two-state protein folding kinetics
-
Plaxco KW, Simons KT, Ruczinski I, Baker D. Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry 2000;39:11177-11183.
-
(2000)
Biochemistry
, vol.39
, pp. 11177-11183
-
-
Plaxco, K.W.1
Simons, K.T.2
Ruczinski, I.3
Baker, D.4
-
19
-
-
0033613255
-
Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
-
Alm E, Baker D. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc Natl Acad Sci USA 1999;96:11305-11310.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 11305-11310
-
-
Alm, E.1
Baker, D.2
-
20
-
-
0033613165
-
A simple model for calculating the kinetics of protein folding from three-dimensional structures
-
Muñoz V, Eaton WA. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc Natl Acad Sci USA 1999;96:11311-11316.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 11311-11316
-
-
Muñoz, V.1
Eaton, W.A.2
-
21
-
-
0033521194
-
First principles prediction of protein folding rates
-
Debe DA, Goddard WA. First principles prediction of protein folding rates. J Mol Biol 1999;294:619-625.
-
(1999)
J Mol Biol
, vol.294
, pp. 619-625
-
-
Debe, D.A.1
Goddard, W.A.2
-
22
-
-
0037133574
-
How the folding rate constant of simple, single-domain proteins depends on the number of native contacts
-
Makarov DE, Keller CA, Plaxco KW, Metiu H. How the folding rate constant of simple, single-domain proteins depends on the number of native contacts. Proc Natl Acad Sci USA 2002;99:3535-3539.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 3535-3539
-
-
Makarov, D.E.1
Keller, C.A.2
Plaxco, K.W.3
Metiu, H.4
-
23
-
-
0029155772
-
Impact of local and nonlocal interactions on thermodynamics and kinetics of protein folding
-
Abkevich VI, Gutin AM, Shakhnovich EI. Impact of local and nonlocal interactions on thermodynamics and kinetics of protein folding. J Mol Biol 1995;252:460-471.
-
(1995)
J Mol Biol
, vol.252
, pp. 460-471
-
-
Abkevich, V.I.1
Gutin, A.M.2
Shakhnovich, E.I.3
-
24
-
-
0037044965
-
Topological complexity, contact order, and protein folding rates
-
Faisca PFN, Ball RC. Topological complexity, contact order, and protein folding rates. J Chem Phys 2002;117:8587-8591.
-
(2002)
J Chem Phys
, vol.117
, pp. 8587-8591
-
-
Faisca, P.F.N.1
Ball, R.C.2
-
25
-
-
0035850732
-
Roles of native topology and chain-length scaling in protein folding: A simulation study with a Gō-like model
-
Koga N, Takada S. Roles of native topology and chain-length scaling in protein folding: a simulation study with a Gō-like model. J Mol Biol 2001;313:171-180.
-
(2001)
J Mol Biol
, vol.313
, pp. 171-180
-
-
Koga, N.1
Takada, S.2
-
26
-
-
0037216990
-
Universality classes in folding times of proteins
-
Cieplak M, Hoang TX. Universality classes in folding times of proteins. Biophys J 2003;84:475-488.
-
(2003)
Biophys J
, vol.84
, pp. 475-488
-
-
Cieplak, M.1
Hoang, T.X.2
-
27
-
-
0037423710
-
Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates
-
Jewett AI, Pande VS, Plaxco KW. Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates. J Mol Biol 2003;326:247-253.
-
(2003)
J Mol Biol
, vol.326
, pp. 247-253
-
-
Jewett, A.I.1
Pande, V.S.2
Plaxco, K.W.3
-
28
-
-
0037181484
-
The chicken-egg scenario of protein folding revisited
-
Uversky VN, Fink AL. The chicken-egg scenario of protein folding revisited. FEBS Lett 2002;515:79-83.
-
(2002)
FEBS Lett
, vol.515
, pp. 79-83
-
-
Uversky, V.N.1
Fink, A.L.2
-
29
-
-
0032972986
-
Is protein folding hierarchic? I. Local structure and peptide folding
-
Baldwin RL, Rose GD. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem Sci 1999;24:26-33.
-
(1999)
Trends Biochem Sci
, vol.24
, pp. 26-33
-
-
Baldwin, R.L.1
Rose, G.D.2
-
30
-
-
0036136694
-
Composites of local structure propensities: Evidence for local encoding of long-range structure
-
Shortle D. Composites of local structure propensities: evidence for local encoding of long-range structure. Protein Sci 2002;11:18-26.
-
(2002)
Protein Sci
, vol.11
, pp. 18-26
-
-
Shortle, D.1
-
31
-
-
0000355428
-
Respective roles of short- and long-range interactions in protein folding
-
Gō N, Taketomi H. Respective roles of short- and long-range interactions in protein folding. Proc Natl Acad Sci USA 1978;75:559-563.
-
(1978)
Proc Natl Acad Sci USA
, vol.75
, pp. 559-563
-
-
Go, N.1
Taketomi, H.2
-
32
-
-
0025370815
-
Dominant forces in protein folding
-
Dill KA. Dominant forces in protein folding. Biochemistry 1990;29:7133-7155.
-
(1990)
Biochemistry
, vol.29
, pp. 7133-7155
-
-
Dill, K.A.1
-
33
-
-
0029865623
-
Context-dependent secondary structure formation of a designed protein sequence
-
Minor DL, Kim PS. Context-dependent secondary structure formation of a designed protein sequence. Nature 1996;380:730-734.
-
(1996)
Nature
, vol.380
, pp. 730-734
-
-
Minor, D.L.1
Kim, P.S.2
-
34
-
-
0036139188
-
Probabilistic sampling of protein conformations: New hope for brute force?
-
Feldman HJ, Hogue CWV. Probabilistic sampling of protein conformations: new hope for brute force? Proteins 2002;46:8-23.
-
(2002)
Proteins
, vol.46
, pp. 8-23
-
-
Feldman, H.J.1
Hogue, C.W.V.2
-
35
-
-
0036891682
-
Origins of protein denatured state compactness and hydrophobic clustering in aqueous urea: Inferences from nonpolar potentials of mean force
-
Shimizu S, Chan HS. Origins of protein denatured state compactness and hydrophobic clustering in aqueous urea: inferences from nonpolar potentials of mean force. Proteins 2002;49:560-566.
-
(2002)
Proteins
, vol.49
, pp. 560-566
-
-
Shimizu, S.1
Chan, H.S.2
-
36
-
-
18344391877
-
Protein structures and optimal folding from a geometrical variational principle
-
Micheletti C, Banavar JR, Maritan A, Seno F. Protein structures and optimal folding from a geometrical variational principle. Phys Rev Lett 1999;82:3372-3375.
-
(1999)
Phys Rev Lett
, vol.82
, pp. 3372-3375
-
-
Micheletti, C.1
Banavar, J.R.2
Maritan, A.3
Seno, F.4
-
37
-
-
0034685604
-
Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
-
Clementi C, Nymeyer H, Onuchic JN. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J Mol Biol 2000;298:937-953.
-
(2000)
J Mol Biol
, vol.298
, pp. 937-953
-
-
Clementi, C.1
Nymeyer, H.2
Onuchic, J.N.3
-
38
-
-
0037113227
-
The role of sidechain packing and native contact interactions in folding: Discontinuous molecular dynamics folding simulations of an all-atom Gō model of fragment B of Staphylococcal protein A
-
Linhananta A, Zhou Y. The role of sidechain packing and native contact interactions in folding: discontinuous molecular dynamics folding simulations of an all-atom Gō model of fragment B of Staphylococcal protein A. J Chem Phys 2002;117:8983-8995.
-
(2002)
J Chem Phys
, vol.117
, pp. 8983-8995
-
-
Linhananta, A.1
Zhou, Y.2
-
39
-
-
0027484016
-
Local and nonlocal interactions in globular proteins and mechanisms of alcohol denaturation
-
Thomas PD, Dill KA. Local and nonlocal interactions in globular proteins and mechanisms of alcohol denaturation. Protein Sci 1993;2:2050-2065.
-
(1993)
Protein Sci
, vol.2
, pp. 2050-2065
-
-
Thomas, P.D.1
Dill, K.A.2
-
40
-
-
0029809182
-
On the origin of the cooperativity of protein folding: Implications from model simulations
-
Kolinski A, Galazka W, Skolnick J. On the origin of the cooperativity of protein folding: implications from model simulations. Proteins 1996;26:271-287.
-
(1996)
Proteins
, vol.26
, pp. 271-287
-
-
Kolinski, A.1
Galazka, W.2
Skolnick, J.3
-
41
-
-
0007463680
-
Statistical mechanics of a correlated energy landscape model for protein folding funnels
-
Plotkin SS, Wang J, Wolynes PG. Statistical mechanics of a correlated energy landscape model for protein folding funnels. J Chem Phys 1997;106:2932-2948.
-
(1997)
J Chem Phys
, vol.106
, pp. 2932-2948
-
-
Plotkin, S.S.1
Wang, J.2
Wolynes, P.G.3
-
42
-
-
0001181898
-
United-residue force field for off-lattice protein structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials
-
Liwo A, Kazmierkiewicz R, Czaplewski C, Groth M, Oldziej S, Wawak RJ, Rackovsky S, Pincus MR, Scheraga HA. United-residue force field for off-lattice protein structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials. J Comput Chem 1998;19:259-276.
-
(1998)
J Comput Chem
, vol.19
, pp. 259-276
-
-
Liwo, A.1
Kazmierkiewicz, R.2
Czaplewski, C.3
Groth, M.4
Oldziej, S.5
Wawak, R.J.6
Rackovsky, S.7
Pincus, M.R.8
Scheraga, H.A.9
-
43
-
-
0032606941
-
Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer
-
Takada S, Luthey-Schulten Z, Wolynes PG. Folding dynamics with nonadditive forces: a simulation study of a designed helical protein and a random heteropolymer. J Chem Phys 1999;110:11616-11629.
-
(1999)
J Chem Phys
, vol.110
, pp. 11616-11629
-
-
Takada, S.1
Luthey-Schulten, Z.2
Wolynes, P.G.3
-
44
-
-
0035826032
-
Role of explicitly cooperative interactions in protein folding funnels: A simulation study
-
Eastwood MP, Wolynes PG. Role of explicitly cooperative interactions in protein folding funnels: a simulation study. J Chem Phys 2001;114:4702-4716.
-
(2001)
J Chem Phys
, vol.114
, pp. 4702-4716
-
-
Eastwood, M.P.1
Wolynes, P.G.2
-
45
-
-
0001193711
-
The effect of internal constraints on the configurations of chain molecules
-
Erratum: J Chem Phys 1997;107:10353
-
Chan HS, Dill KA. The effect of internal constraints on the configurations of chain molecules. J Chem Phys 1990;92:3118-3135 [Erratum: J Chem Phys 1997;107:10353].
-
(1990)
J Chem Phys
, vol.92
, pp. 3118-3135
-
-
Chan, H.S.1
Dill, K.A.2
-
46
-
-
0013527261
-
Perspectives on protein evolution from simple exact models
-
Chan HS, Bornberg-Bauer E. Perspectives on protein evolution from simple exact models. Appl Bioinformatics 2002;1:121-144.
-
(2002)
Appl Bioinformatics
, vol.1
, pp. 121-144
-
-
Chan, H.S.1
Bornberg-Bauer, E.2
-
47
-
-
0001229818
-
Temperature dependence of the folding rate in a simple protein model: Search for a "glass" transition
-
Gutin A, Sali A, Abkevich V, Karplus M, Shakhnovich EI. Temperature dependence of the folding rate in a simple protein model: search for a "glass" transition. J Chem Phys 1998;108:6466-6483.
-
(1998)
J Chem Phys
, vol.108
, pp. 6466-6483
-
-
Gutin, A.1
Sali, A.2
Abkevich, V.3
Karplus, M.4
Shakhnovich, E.I.5
-
48
-
-
0023517017
-
Effect of point mutations on the folding of globular proteins
-
Matthews CR. Effect of point mutations on the folding of globular proteins. Methods Enzymol 1987;154:498-511.
-
(1987)
Methods Enzymol
, vol.154
, pp. 498-511
-
-
Matthews, C.R.1
-
49
-
-
36448999595
-
Free energy landscape for protein folding kinetics: Intermediates, traps, and multiple pathways in theory and lattice model simulations
-
Abkevich VI, Gutin AM, Shakhnovich EI. Free energy landscape for protein folding kinetics: intermediates, traps, and multiple pathways in theory and lattice model simulations. J Chem Phys 1994;101:6052-6062.
-
(1994)
J Chem Phys
, vol.101
, pp. 6052-6062
-
-
Abkevich, V.I.1
Gutin, A.M.2
Shakhnovich, E.I.3
-
51
-
-
0036215854
-
Folding rate prediction using total contact distance
-
Zhou HY, Zhou YQ. Folding rate prediction using total contact distance. Biophys J 2002;82:458-463.
-
(2002)
Biophys J
, vol.82
, pp. 458-463
-
-
Zhou, H.Y.1
Zhou, Y.Q.2
-
53
-
-
0036667731
-
Rotamer libraries in the 21st century
-
Dunbrack RL. Rotamer libraries in the 21st century. Curr Opin Struct Biol 2002;12:431-440.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 431-440
-
-
Dunbrack, R.L.1
-
54
-
-
0036643497
-
Anti-cooperativity and cooperativity in hydrophobic interactions: Three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins
-
Erratum: Proteins 2002;49:294
-
Shimizu S, Chan HS. Anti-cooperativity and cooperativity in hydrophobic interactions: three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins. Proteins 2002;48:15-30. [Erratum: Proteins 2002;49:294].
-
(2002)
Proteins
, vol.48
, pp. 15-30
-
-
Shimizu, S.1
Chan, H.S.2
-
55
-
-
0037375366
-
Prediction of folding rates and transition-state placement from native-state geometry
-
Micheletti C. Prediction of folding rates and transition-state placement from native-state geometry. Proteins 2003;51:74-84.
-
(2003)
Proteins
, vol.51
, pp. 74-84
-
-
Micheletti, C.1
|